1
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Swenson CS, Lackey HH, Reece EJ, Harris JM, Heemstra JM, Peterson EM. Evaluating the effect of ionic strength on PNA:DNA duplex formation kinetics. RSC Chem Biol 2021; 2:1249-1256. [PMID: 34458838 PMCID: PMC8341200 DOI: 10.1039/d1cb00025j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/07/2021] [Indexed: 11/21/2022] Open
Abstract
Peptide nucleic acid (PNA) is a unique synthetic nucleic acid analog that has been adopted for use in many biological applications. These applications rely upon the robust Franklin-Watson-Crick base pairing provided by PNA, particularly at lower ionic strengths. However, our understanding of the relationship between the kinetics of PNA:DNA hybridization and ionic strength is incomplete. Here we measured the kinetics of association and dissociation of PNA with DNA across a range of ionic strengths and temperatures at single-molecule resolution using total internal reflection fluorescence imaging. Unlike DNA:DNA duplexes, PNA:DNA duplexes are more stable at lower ionic strength, and we demonstrate that this is due to a higher association rate. While the dissociation rate of PNA:DNA duplexes is largely insensitive to ionic strength, it is significantly lower than that of DNA:DNA duplexes having the same number and sequence of base pairing interactions. The temperature dependence of PNA:DNA kinetic rate constants indicate a significant enthalpy barrier to duplex dissociation, and to a lesser extent, duplex formation. This investigation into the kinetics of PNA:DNA hybridization provides a framework towards better understanding and design of PNA sequences for future applications.
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Affiliation(s)
- Colin S Swenson
- Department of Chemistry, Emory University Atlanta GA 30322 USA
| | - Hershel H Lackey
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| | - Eric J Reece
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| | - Joel M Harris
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| | | | - Eric M Peterson
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
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2
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Abstract
Hybridization between nucleic acid strands immobilized on a solid support with partners in solution is widely practiced in bioanalytical technologies and materials science. An important fundamental aspect of understanding these reactions is the role played by immobilization in the dynamics of duplex formation and disassembly. This report reviews and analyzes literature kinetic data to identify commonly observed trends and to correlate them with probable molecular mechanisms. The analysis reveals that while under certain conditions impacts from immobilization are minimal so that surface and solution hybridization kinetics are comparable, it is more typical to observe pronounced offsets between the two scenarios. In the forward (hybridization) direction, rates at the surface commonly decrease by one to two decades relative to solution, while in the reverse direction rates of strand separation at the surface can exceed those in solution by tens of decades. By recasting the deviations in terms of activation barriers, a consensus of how immobilization impacts nucleation, zipping, and strand separation can be conceived within the classical mechanism in which duplex formation is rate limited by preassembly of a nucleus a few base pairs in length, while dehybridization requires the cumulative breakup of base pairs along the length of a duplex. Evidence is considered for how excess interactions encountered on solid supports impact these processes.
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Affiliation(s)
- Eshan Treasurer
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Rastislav Levicky
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
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3
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Su S, Ma J, Xu Y, Pan H, Zhu D, Chao J, Weng L, Wang L. Electrochemical Analysis of Target-Induced Hairpin-Mediated Aptamer Sensors. ACS APPLIED MATERIALS & INTERFACES 2020; 12:48133-48139. [PMID: 32955243 DOI: 10.1021/acsami.0c12897] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The state of probe DNA at the biosensing interface greatly affects the detection performance of electrochemical DNA biosensors. Herein, we constructed a target-induced hairpin-mediated biosensing interface to study the effect of probe DNA on the analytical performance of adenosine triphosphate aptamer (ATPA) and adenosine triphosphate (ATP) detection. Moreover, we also explored the electrochemical contribution of the coexisting hairpin and double-stranded DNA (dsDNA) to this sensing interface. Experimental results suggested that the molecular recognition ability and detection performance of the biosensing interface were majorly dependent on the surface density of methylene blue (MB)-labeled probe hairpin DNA and partly affected by the spatial state of the formed dsDNA. When the surface density of hairpin DNA was moderate (5.72 pmol cm-2), this sensing interface determined as low as 0.74 fM ATPA and 5.04 pM ATP with high selectivity and excellent regeneration, respectively. Furthermore, we calculated that the formed dsDNA had a 31.87% contribution in the total electrochemical signal for 10 pM ATPA detection. Based on the above results, we designed an XOR logic gate based on the biosensing interface for ATPA and ATP detection.
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Affiliation(s)
- Shao Su
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jianfeng Ma
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Yongqiang Xu
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Hemeng Pan
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Dan Zhu
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jie Chao
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Lixing Weng
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
- College of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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4
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Practical Synthesis of Quinoline-Protected Morpholino Oligomers for Light-Triggered Regulation of Gene Function. Molecules 2020; 25:molecules25092078. [PMID: 32365635 PMCID: PMC7248704 DOI: 10.3390/molecules25092078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/13/2020] [Accepted: 04/22/2020] [Indexed: 11/21/2022] Open
Abstract
Photoactivatable cyclic caged morpholino oligomers (ccMOs) represent a promising tool to selectively regulate gene expression with spatiotemporal control. Nevertheless, some challenges associated with the preparation of these reagents have limited their broader use in biological settings. We describe a novel ccMO design that overcomes many of the challenges and considerably expedites the synthetic preparation. The key factor is the introduction of an ethynyl function on the photocleavable linker to facilitate the use of a Huisgen 1,3-dipolar cycloaddition for the coupling reaction with the oligonucleotide. Compared to previous strategies, this modification reduces the number of synthetic steps and significantly improves the total yield and the stability of the linker. We used the alkynyl-functionalized linker for the preparation of two different ccMOs targeting the mRNA of the glutamic acid decarboxylase genes, gad1 and gad2. HPLC analysis confirms that the caging strategy successfully inhibits the DNA binding ability, and the activity can be restored by brief illumination with 405-nm light. Overall, the straightforward preparation together with the clean and fast photochemistry make these caged antisense reagents excellent tools to modulate gene function in-vivo with spatial and temporal precision.
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5
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Langford GJ, Raeburn J, Ferrier DC, Hands PJW, Shaver MP. Morpholino Oligonucleotide Cross-Linked Hydrogels as Portable Optical Oligonucleotide Biosensors. ACS Sens 2019; 4:185-191. [PMID: 30592402 DOI: 10.1021/acssensors.8b01208] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Morpholino Oligonucleotides (MOs), an uncharged DNA analogue, are functionalized with an acrylamide moiety and incorporated into polymer hydrogels as responsive cross-links for microRNA sequence detection. The MO cross-links can be selectively cleaved by a short target analyte single-stranded DNA (ssDNA) sequence based on microRNA, inducing a distinct swelling response measured optically. The MO cross-links offer significant improvement over DNA based systems through improved thermal stability, no salt requirement and 1000-fold improved sensitivity over a comparative biosensor, facilitating a wider range of sensing conditions. Analysis was also achieved using a mobile phone camera, demonstrating portability.
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Affiliation(s)
- Geraint J. Langford
- School of Chemistry, David Brewster Road, University of Edinburgh, Edinburgh, EH9 3FJ, United Kingdom
| | - Jaclyn Raeburn
- School of Chemistry, David Brewster Road, University of Edinburgh, Edinburgh, EH9 3FJ, United Kingdom
| | - David C. Ferrier
- Institute for Integrated Micro and Nano Systems, School of Engineering, University of Edinburgh, Edinburgh, EH9 3JL, United Kingdom
| | - Philip J. W. Hands
- Institute for Integrated Micro and Nano Systems, School of Engineering, University of Edinburgh, Edinburgh, EH9 3JL, United Kingdom
| | - Michael P. Shaver
- School of Chemistry, David Brewster Road, University of Edinburgh, Edinburgh, EH9 3FJ, United Kingdom
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6
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Gu Q, Nanney W, Cao HH, Wang H, Ye T. Single Molecule Profiling of Molecular Recognition at a Model Electrochemical Biosensor. J Am Chem Soc 2018; 140:14134-14143. [PMID: 30293418 DOI: 10.1021/jacs.8b07325] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The spatial arrangement of target and probe molecules on the biosensor is a key aspect of the biointerface structure that ultimately determines the properties of interfacial molecular recognition and the performance of the biosensor. However, the spatial patterns of single molecules on practical biosensors have been unknown, making it difficult to rationally engineer biosensors. Here, we have used high-resolution atomic force microscopy to map closely spaced individual probes as well as discrete hybridization events on a functioning electrochemical DNA sensor surface. We also applied spatial statistical methods to characterize the spatial patterns at the single molecule level. We observed the emergence of heterogeneous spatiotemporal patterns of surface hybridization of hairpin probes. The clustering of target capture suggests that hybridization may be enhanced by proximity of probes and targets that are about 10 nm away. The unexpected enhancement was rationalized by the complex interplay between the nanoscale spatial organization of probe molecules, the conformational changes of the probe molecules, and target binding. Such molecular level knowledge may allow one to tailor the spatial patterns of the biosensor surfaces to improve the sensitivity and reproducibility.
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7
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Stirmanov YV, Matveeva OV, Nechipurenko YD. Two-dimensional Ising model for microarray hybridization: cooperative interactions between bound target molecules. J Biomol Struct Dyn 2018; 37:3103-3108. [PMID: 30081753 DOI: 10.1080/07391102.2018.1508370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The Langmuir adsorption model is widely used for description and quantification of microarray oligo-target hybridization. According to the model, the binding centers for adsorption of target molecules from solution are represented by oligo-probes. However, the Langmuir model does not consider the interactions between the targets adsorbed at the neighboring binding centers, which are possible due to high-density of array-bound probes. We have shown that the two-dimensional Ising model, which takes into account the nearest neighboring target molecules interactions, better describes the experimental data of oligo-target hybridization in comparison with the Langmuir model. Thus, we found an evidence for existence of positive cooperative interactions between adsorbed target molecules: so, binding of the first target molecules facilitates the binding of subsequent ones to the neighboring probes. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Y V Stirmanov
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , Moscow , Russia
| | - O V Matveeva
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , Moscow , Russia
| | - Y D Nechipurenko
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , Moscow , Russia
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8
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Chiadò A, Novara C, Lamberti A, Geobaldo F, Giorgis F, Rivolo P. Immobilization of Oligonucleotides on Metal-Dielectric Nanostructures for miRNA Detection. Anal Chem 2016; 88:9554-9563. [DOI: 10.1021/acs.analchem.6b02186] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Alessandro Chiadò
- Department
of Applied Science
and Technology, Politecnico di Torino, C.so Duca degli Abruzzi 24 10129, Torino, Italy
| | - Chiara Novara
- Department
of Applied Science
and Technology, Politecnico di Torino, C.so Duca degli Abruzzi 24 10129, Torino, Italy
| | - Andrea Lamberti
- Department
of Applied Science
and Technology, Politecnico di Torino, C.so Duca degli Abruzzi 24 10129, Torino, Italy
| | - Francesco Geobaldo
- Department
of Applied Science
and Technology, Politecnico di Torino, C.so Duca degli Abruzzi 24 10129, Torino, Italy
| | - Fabrizio Giorgis
- Department
of Applied Science
and Technology, Politecnico di Torino, C.so Duca degli Abruzzi 24 10129, Torino, Italy
| | - Paola Rivolo
- Department
of Applied Science
and Technology, Politecnico di Torino, C.so Duca degli Abruzzi 24 10129, Torino, Italy
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9
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Qiao W, Chiang HC, Xie H, Levicky R. Surface vs. solution hybridization: effects of salt, temperature, and probe type. Chem Commun (Camb) 2016; 51:17245-8. [PMID: 26459915 DOI: 10.1039/c5cc06674c] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hybridization thermodynamics on solid supports are compared with those in solution for two types of hybridization probe, DNA and uncharged morpholino oligonucleotides of identical sequences. Trends in hybridization affinity are discussed with respect to ionic strength, temperature, and surface behavior.
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Affiliation(s)
- Wanqiong Qiao
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Hao-Chun Chiang
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Hui Xie
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Rastislav Levicky
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
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10
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He Y, Zhang J, Ruffin S, Ji L, Wang K, Levicky R, Xia X. An Electrochemical Study of the Surface Hybridization Process of Morpholino-DNA: Thermodynamics and Kinetics. ELECTROANAL 2016. [DOI: 10.1002/elan.201501109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yakai He
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing, Jiangsu 163 Xianlin Avenue 210023 P. R. China
| | - Jing Zhang
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing, Jiangsu 163 Xianlin Avenue 210023 P. R. China
| | - Sade Ruffin
- Department of Chemical and Biomolecular Engineering; New York University Polytechnic School of Engineering; 6 MetroTech Center Brooklyn, New York 11201
| | - Lina Ji
- State Key Laboratory of Pharmaceutical Biotechnology; School of Life Sciences; Nanjing University; Nanjing, Jiangsu 163 Xianlin Avenue 210023 P. R. China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing, Jiangsu 163 Xianlin Avenue 210023 P. R. China
| | - Rastislav Levicky
- Department of Chemical and Biomolecular Engineering; New York University Polytechnic School of Engineering; 6 MetroTech Center Brooklyn, New York 11201
| | - Xinghua Xia
- State Key Laboratory of Analytical Chemistry for Life Science; School of Chemistry and Chemical Engineering; Nanjing University; Nanjing, Jiangsu 163 Xianlin Avenue 210023 P. R. China
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11
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Challier L, Miranda-Castro R, Marchal D, Noël V, Mavré F, Limoges B. Kinetic Rotating Droplet Electrochemistry: A Simple and Versatile Method for Reaction Progress Kinetic Analysis in Microliter Volumes. J Am Chem Soc 2013; 135:14215-28. [DOI: 10.1021/ja405415q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Lylian Challier
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Rebeca Miranda-Castro
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Damien Marchal
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Vincent Noël
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - François Mavré
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Benoît Limoges
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
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12
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Cao L, Zhao Y, Ji LN, Zhang J, Wang K, Xia XH. The Enhanced Enzymolysis Resistance of Surface-Immobilized DNA Caused by Hybridizing with Morpholino. ELECTROANAL 2013. [DOI: 10.1002/elan.201200612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Zhao Y, Cao L, Ouyang J, Wang M, Wang K, Xia XH. Reversible plasmonic probe sensitive for pH in micro/nanospaces based on i-motif-modulated morpholino-gold nanoparticle assembly. Anal Chem 2012; 85:1053-7. [PMID: 23215633 DOI: 10.1021/ac302915a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Exploring local pH in micro/nanoscale is fundamentally important for understanding microprocesses including the corrosion of metal and the metabolism of cell. Regular fluorescence pH probes and potentiometric electrodes show either low signal intensity or lack of spatial resolution when being applied in a micro/nanoenvironment. Here, we developed a nanoscale reversible pH probe based on the plasmonic coupling effect of i-motif modulated gold nanoparticle (AuNP) assembly. The pH probe shows a reversible and highly sensitive response to pH variation between 4.5 and 7.5. Introduction of morpholino oligomers (MO), a neutral analog of DNA, into the assembly endows the pH probe with high stability even under low salt concentration. The intense optical signal of a AuNP enables local pH to be read out not only in the micro/nanofluidic channel but also on a single i-motif-MO-AuNP assembly. Recording of the strong plasmonic resonance scattering spectrum of AuNP provides a promising method for extracting chemical information in nanospace of biological systems.
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Affiliation(s)
- Yun Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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14
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Qiao W, Kalachikov S, Liu Y, Levicky R. Charge-neutral morpholino microarrays for nucleic acid analysis. Anal Biochem 2012; 434:207-14. [PMID: 23246344 DOI: 10.1016/j.ab.2012.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 11/21/2012] [Accepted: 12/03/2012] [Indexed: 12/14/2022]
Abstract
A principal challenge in microarray experiments is to facilitate hybridization between probe strands on the array with complementary target strands from solution while suppressing any competing interactions that the probes and targets may experience. Synthetic DNA analogs, whose hybridization to targets can exhibit qualitatively different dependence on experimental conditions than for nucleic acid probes, open up an attractive alternative for improving selectivity of array hybridization. Morpholinos (MOs), a class of uncharged DNA analogs, are investigated as microarray probes instead of DNA. MO microarrays were fabricated by contact printing of amino-modified probes onto aldehyde slides. In addition to covalent immobilization, MOs were found to efficiently immobilize through physical adsorption; such physically adsorbed probes could be removed by post-printing washes with surfactant solutions. Hybridization of double-stranded DNA targets to MO microarrays revealed a hybridization maximum at intermediate ionic strengths. The decline in hybridization at lower ionic strengths was attributed to an electrostatic barrier accumulated from hybridized DNA targets, whereas at higher ionic strengths it was attributed to stabilization of target secondary structure in solution. These trends, which illustrate ionic strength tuning of forming on-array relative to solution secondary structure, were supported by a stability analysis of MO/DNA and DNA/DNA duplexes in solution.
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Affiliation(s)
- Wanqiong Qiao
- Department of Chemical and Biomolecular Engineering, Polytechnic Institute of New York University, Brooklyn, NY 11201, USA
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15
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Breuer R, Schmittel M. Redox-Stable SAMs in Water (pH 0–12) from 1,1′-Biferrocenylene-Terminated Thiols on Gold. Organometallics 2012. [DOI: 10.1021/om300718k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Rochus Breuer
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I, Universität Siegen, Adolf-Reichwein-Straße
2, D-57068 Siegen, Germany
| | - Michael Schmittel
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I, Universität Siegen, Adolf-Reichwein-Straße
2, D-57068 Siegen, Germany
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16
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Anne A, Chovin A, Demaille C. Optimizing electrode-attached redox-peptide systems for kinetic characterization of protease action on immobilized substrates. Observation of dissimilar behavior of trypsin and thrombin enzymes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:8804-8813. [PMID: 22591015 DOI: 10.1021/la301316r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this work, we experimentally address the issue of optimizing gold electrode attached ferrocene (Fc)-peptide systems for kinetic measurements of protease action. Considering human α-thrombin and bovine trypsin as proteases of interest, we show that the recurring problem of incomplete cleavage of the peptide layer by these enzymes can be solved by using ultraflat template-stripped gold, instead of polished polycrystalline gold, as the Fc-peptide bearing electrode material. We describe how these fragile surfaces can be mounted in a rotating disk configuration so that enzyme mass transfer no longer limits the overall measured cleavage kinetics. Finally, we demonstrate that, once the system has been optimized, in situ real-time cyclic voltammetry monitoring of the protease action can yield high-quality kinetic data, showing no sign of interfering effects. The cleavage progress curves then closely match the Langmuirian variation expected for a kinetically controlled surface process. Global fit of the progress curves yield accurate values of the peptide cleavage rate for both trypsin and thrombin. It is shown that, whereas trypsin action on the surface-attached peptide closely follows Michaelis-Menten kinetics, thrombin displays a specific and unexpected behavior characterized by a nearly enzyme-concentration-independent cleavage rate in the subnanomolar enzyme concentration range. The reason for this behavior has still to be clarified, but its occurrence may limit the sensitivity of thrombin sensors based on Fc-peptide layers.
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Affiliation(s)
- Agnès Anne
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Univ Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France.
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17
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Ge D, Wang X, Williams K, Levicky R. Thermostable DNA immobilization and temperature effects on surface hybridization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:8446-8455. [PMID: 22578171 PMCID: PMC3368703 DOI: 10.1021/la301165a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Monolayer films of nucleic acids on solid supports are encountered in a range of diagnostic and bioanalytical applications. These applications often rely on elevated temperatures to improve performance; moreover, studies at elevated temperatures can provide fundamental information on layer organization and functionality. To support such applications, this study compares thermostability of oligonucleotide monolayers immobilized to gold by first coating the gold with a nanometer-thick film (an "anchor layer") of a polymercaptosiloxane, to which DNA oligonucleotides are subsequently tethered through maleimide-thiol conjugation, with thermostability of monolayers formed via widely used attachment through a terminal thiol moiety on the DNA. The temperature range covered is from 25 to 90 °C. After confirming stability of immobilization and, more importantly, retention of hybridization activity even under the harshest conditions investigated, these thermostable films are used to demonstrate measurements of (1) reversible surface melting transitions and (2) temperature dependence of competitive hybridization, when fully matched and mismatched sequences compete for binding to immobilized DNA oligonucleotides. The competitive hybridization experiments reveal a pronounced impact of temperature on rates of approach to equilibrium, with kinetic freezing into nonequilibrium states close to room temperature and rapid approach to equilibrium at elevated temperatures. Modeling of competitive surface hybridization equilibria using thermodynamic parameters derived from surface melting transitions of the individual sequences is also discussed.
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